def do(self):
graph = create_molecular_graph(context.application.cache.nodes)
match_generator = GraphSearch(RingPattern(20))
rings = list(match_generator(graph))
ring_distribution_window = RingDistributionWindow()
ring_distribution_window.show(rings, graph)
def do(self):
cache = context.application.cache
graph = create_molecular_graph(cache.nodes)
parent = cache.node
Frame = context.application.plugins.get_node("Frame")
for group in graph.independent_vertices:
atoms = [graph.molecule.atoms[i] for i in group]
new_positions = self.calc_new_positions(group, atoms, graph,
parent)
if new_positions is None:
# this happens for groups of atoms that are inherently periodic.
continue
frame = Frame(name=chemical_formula(atoms)[1])
primitive.Add(frame, parent, index=0)
for node, atom in zip(group, atoms):
primitive.Move(atom, frame)
new_position = new_positions[node]
translation = Translation(
atom.get_parentframe_up_to(parent).inv * new_position)
primitive.SetProperty(atom, "transformation", translation)
for atom in atoms:
# take a copy of the references since they are going to be
# refreshed (changed and reverted) during the loop.
for reference in list(atom.references):
referent = reference.parent
if referent.parent != frame:
has_to_move = True
for child in referent.children:
if child.target.parent != frame:
has_to_move = False
break
if has_to_move:
primitive.Move(referent, frame)
def do(self):
cache = context.application.cache
graph = create_molecular_graph(cache.nodes)
parent = cache.node
Frame = context.application.plugins.get_node("Frame")
for group in graph.independent_nodes:
atoms = [graph.molecule.atoms[i] for i in group]
new_positions = self.calc_new_positions(group, atoms, graph, parent)
frame = Frame(name=chemical_formula(atoms)[1])
primitive.Add(frame, parent, index=0)
for node, atom in zip(group, atoms):
primitive.Move(atom, frame)
new_position = new_positions[node]
translation = Translation()
translation.t = atom.get_parentframe_up_to(parent).vector_apply_inverse(new_position)
primitive.SetProperty(atom, "transformation", translation)
for atom in atoms:
# take a copy of the references since they are going to be
# refreshed (changed and reverted) during the loop.
for reference in copy.copy(atom.references):
referent = reference.parent
if referent.parent != frame:
has_to_move = True
for child in referent.children:
if child.target.parent != frame:
has_to_move = False
break
if has_to_move:
primitive.Move(referent, frame)
def do(self):
frame_ref = context.application.cache.nodes[0]
graph_ref = create_molecular_graph([frame_ref])
try:
match_generator = GraphSearch(EqualPattern(graph_ref))
except PatternError, e:
raise UserError("Could not setup a graph match definition to clone the order.")
def do(self):
graph = create_molecular_graph(context.application.cache.nodes)
match_generator = GraphSearch(RingPattern(20))
rings = list(match_generator(graph))
ring_distribution_window = RingDistributionWindow()
ring_distribution_window.show(rings, graph)
def do(self):
for key, val in self.parameters.__dict__.iteritems():
if isinstance(val, Expression):
val.compile_as("<%s>" % key)
val.variables = (key[7:11], )
parent = context.application.cache.common_parent
if parent is None:
parent = context.application.model.universe
angles = []
graph = create_molecular_graph(context.application.cache.nodes)
match_definition = BendingAnglePattern(criteria_sets=[
CriteriaSet(
thing_criteria={
0: IndexToAtoms(self.parameters.filter_atom1),
1: IndexToAtoms(self.parameters.filter_atom2),
2: IndexToAtoms(self.parameters.filter_atom3),
},
relation_criteria={
0: IndexToBonds(self.parameters.filter_bond12),
1: IndexToBonds(self.parameters.filter_bond23),
},
)
], )
try:
atoms = graph.molecule.atoms
match_generator = GraphSearch(match_definition)
for match in match_generator(graph):
point1 = atoms[match.forward[0]].get_absolute_frame().t
point2 = atoms[match.forward[1]].get_absolute_frame().t
point3 = atoms[match.forward[2]].get_absolute_frame().t
delta1 = parent.shortest_vector(point2 - point1)
delta2 = parent.shortest_vector(point2 - point3)
if numpy.linalg.norm(delta1) > 1e-8 and \
numpy.linalg.norm(delta2) > 1e-8:
angles.append(angle(delta1, delta2))
except:
raise UserError(
"An error occured while sampling the bending angles.",
"If this is an error in one of the filter expressions,\n" +
"one should see the expression mentioned below as <filter_...>.\n\n"
)
comments = [
"atom 1 filter expression: %s" % self.parameters.filter_atom1.code,
"bond 1-2 filter expression: %s" %
self.parameters.filter_bond12.code,
"atom 2 filter expression: %s" % self.parameters.filter_atom2.code,
"bond 2-3 filter expression: %s" %
self.parameters.filter_bond23.code,
"atom 3 filter expression: %s" % self.parameters.filter_atom3.code,
]
if len(angles) > 0:
distribution_dialog = DistributionDialog()
distribution_dialog.run(numpy.array(angles), "Angle",
"Bending angle", comments)
else:
raise UserError("No bending angles match the given criteria.")
def do(self):
frame_ref = context.application.cache.nodes[0]
graph_ref = create_molecular_graph([frame_ref])
try:
match_generator = GraphSearch(EqualPattern(graph_ref))
except GraphError, e:
raise UserError(
"Could not setup a graph match definition to clone the order.")
def do(self):
for key, val in self.parameters.__dict__.iteritems():
if isinstance(val, Expression):
val.compile_as("<%s>" % key)
val.variables = (key[7:11],)
parent = context.application.cache.common_parent
if parent is None:
parent = context.application.model.universe
angles = []
graph = create_molecular_graph(context.application.cache.nodes)
match_definition = BendingAnglePattern(
criteria_sets=[CriteriaSet(
thing_criteria={
0: IndexToAtoms(self.parameters.filter_atom1),
1: IndexToAtoms(self.parameters.filter_atom2),
2: IndexToAtoms(self.parameters.filter_atom3),
},
relation_criteria={
0: IndexToBonds(self.parameters.filter_bond12),
1: IndexToBonds(self.parameters.filter_bond23),
},
)],
)
try:
atoms = graph.molecule.atoms
match_generator = GraphSearch(match_definition)
for match in match_generator(graph):
point1 = atoms[match.forward[0]].get_absolute_frame().t
point2 = atoms[match.forward[1]].get_absolute_frame().t
point3 = atoms[match.forward[2]].get_absolute_frame().t
delta1 = parent.shortest_vector(point2 - point1)
delta2 = parent.shortest_vector(point2 - point3)
if numpy.linalg.norm(delta1) > 1e-8 and \
numpy.linalg.norm(delta2) > 1e-8:
angles.append(angle(delta1, delta2))
except:
raise UserError(
"An error occured while sampling the bending angles.",
"If this is an error in one of the filter expressions,\n" +
"one should see the expression mentioned below as <filter_...>.\n\n"
)
comments = [
"atom 1 filter expression: %s" % self.parameters.filter_atom1.code,
"bond 1-2 filter expression: %s" % self.parameters.filter_bond12.code,
"atom 2 filter expression: %s" % self.parameters.filter_atom2.code,
"bond 2-3 filter expression: %s" % self.parameters.filter_bond23.code,
"atom 3 filter expression: %s" % self.parameters.filter_atom3.code,
]
if len(angles) > 0:
distribution_dialog = DistributionDialog()
distribution_dialog.run(numpy.array(angles), "Angle", "Bending angle", comments)
else:
raise UserError("No bending angles match the given criteria.")
def __call__(self, f, universe, folder, nodes=None):
atom_counter = 0
if nodes is None:
nodes = [universe]
graph = create_molecular_graph([universe])
names = [atom.name for atom in graph.molecule.atoms]
charges = [atom.extra.get("charge", 0.0) for atom in graph.molecule.atoms]
psf_file = PSFFile()
psf_file.add_molecular_graph(graph, atom_types=names, charges=charges)
psf_file.dump(f)
def do(self):
# Get the molecular graph of the molecule in the selection
parent = context.application.cache.node
graph = create_molecular_graph([parent], parent)
if graph.molecule.size == 0:
raise UserError("Could not get molecular graph.", "Make sure that the selected frame contains a molecule.")
# Guessed and original geometry
opt_coords = guess_geometry(graph).coordinates
org_coords = graph.molecule.coordinates
coords_to_zeobuilder(org_coords, opt_coords, graph.molecule.atoms, parent)
class CloneOrder(Immediate):
description = "Apply the order of the first selection to all the other."
menu_info = MenuInfo("default/_Object:tools/_Molecular:rearrange",
"_Clone order",
order=(0, 4, 1, 5, 0, 3))
authors = [authors.toon_verstraelen]
@staticmethod
def analyze_selection():
if not Immediate.analyze_selection(): return False
cache = context.application.cache
if len(cache.nodes) < 2: return False
Frame = context.application.plugins.get_node("Frame")
for cls in cache.classes:
if not issubclass(cls, Frame): return False
return True
def do(self):
frame_ref = context.application.cache.nodes[0]
graph_ref = create_molecular_graph([frame_ref])
try:
match_generator = GraphSearch(EqualPattern(graph_ref))
except GraphError, e:
raise UserError(
"Could not setup a graph match definition to clone the order.")
some_failed = False
all_failed = True
for frame_other in context.application.cache.nodes[1:]:
graph_other = create_molecular_graph([frame_other])
try:
match = match_generator(graph_other).next()
all_failed = False
except (StopIteration, GraphError):
some_failed = True
continue
moves = [(index1, graph_other.molecule.atoms[index2])
for index1, index2 in match.forward.iteritems()]
moves.sort()
for new_index, atom2 in moves:
primitive.Move(atom2, frame_other, new_index)
if all_failed:
raise UserError("None of the atom orders could be cloned.")
elif some_failed:
ok_error(
"Some molecules/frames did not match the first frame, so they are not reordered."
)
def do(self):
# Get the molecular graph of the molecule in the selection
parent = context.application.cache.node
graph = create_molecular_graph([parent], parent)
if graph.molecule.size == 0:
raise UserError(
"Could not get molecular graph.",
"Make sure that the selected frame contains a molecule.")
# Guessed and original geometry
opt_coords = tune_geometry(graph, graph.molecule).coordinates
org_coords = graph.molecule.coordinates
coords_to_zeobuilder(org_coords, opt_coords, graph.molecule.atoms,
parent, graph)
def do(self):
# Get the molecular graph of the molecule in the selection
parent = context.application.cache.node
graph = create_molecular_graph([parent], parent)
if graph.molecule.size == 0:
raise UserError("Could not get molecular graph.", "Make sure that the selected frame contains a molecule.")
# Guessed and original geometry
unitcell = context.application.model.universe.cell
unitcell_reciproke = context.application.model.universe.cell_reciproke
unitcell_active = context.application.model.universe.cell_active # not entirely sure where to set this in zeobuilder
opt_coords = guess_geometry(graph, unitcell_active, unitcell, unitcell_reciproke).coordinates
org_coords = graph.molecule.coordinates
coords_to_zeobuilder(org_coords, opt_coords, graph.molecule.atoms, parent, graph)
